An Unlikely Ally
by MetroidMan101
Summary: Are all Space Pirates evil? Samus will find out in a mission that changes her life forever. Renamed from "The Paradox".
1. Mission Impossible

_The Paradox_

Chapter 1: Mission Impossible

Samus entered the bridge of the G.F.S. Olympus with only one thought.

_What do they need this time?_

Admiral Dane glanced back from where he stood.

"We're glad you could come on such short notice. Captain Ferana will fill you in on the mission."

The Galactic Federation Trooper beside him stepped forward. "It seems the Space Pirates have taken over a newly-discovered planet near SR388. We want you to head there and take it back."

"You mean the desert planet? What value does that have?"

Admiral Dane turned on a hologram of a sand-like substance. "This particular mineral was found recently. It can be used to power almost any machine indefinitely, and there are large amounts of it on the planet."

"You want me to capture an entire planet?"

Captain Ferana replied. "I'm going on the mission as well. I have a squad of soldiers that can help you."

Samus nodded. "Fine. I'll prepare."

She turned to leave, but Dane stopped her.

"One more thing. We've detected strange creatures below the surface. Our monitors couldn't see what they were, but it would be wise to make extra preparations."

With that, Samus left the bridge to get ready.

(_End of Chapter_)


	2. Meeting the Team

Chapter 2: Meeting the Team

Samus stared out the window of the ship that was taking her and the strike force to their destination. Captain Ferana sat across from her, talking to his team.

As she watched the group of soldiers, Samus couldn't help but wonder who they were.

"Captain?" She asked. "Who _are_ all of you?"

Ferana replied. "I'm sorry, we didn't introduce ourselves."

The soldier to his right spoke. "I'm Corporal Dennison, and I'm the tech expert."

Next came the pilot in the cockpit. "Sergeant Blaine, at your service."

A soldier sitting beside Samus was the next speaker. "Lieutenant Greene, the explosives master."

The fourth stranger was wearing white armor. "I'm the medic. I'm Private Havis."

One of the men didn't speak. Greene introduced him.

"We call him 'Silent Treatment', but he's our sniper, Specialist Gemaran."

There was one more soldier. He wore red armor and held a rifle. "I'm not part of this group, I'm just here for support. I am Major Coleam."

Captain Ferana nodded. "We are Platoon 83."

Blaine alerted the soldiers. "The planet is just ahead. Thank you for flying with us today!"

An alarm began flashing.

Dennison shouted at the pilot. "Blaine, what's going on?"

"Crap! The pirates are following us! I can't shake 'em!"

As if in response to that, an explosion rocked the ship. Blaine swore.

Coleam ordered. "Everyone, get to the escape pods!"

Samus ran to her ship, which was in the relatively small hanger. She took off and followed Platoon 83 as they abandoned ship in their pods and descended to the planet's surface.

(_End of Chapter_)

**Author's Note: Next chapter will be longer! I promise!**


	3. The Meeting

Chapter 3: The Meeting

**Author's Note: OH MY GOD! WRITER'S BLOCK FOR OVER A MONTH! Sorry for the wait, but I appear to have grown more popular while I was gone! Anyway, back to the story. Lights, camera, action!**

Samus ducked behind a large rock, the air hot with laser blasts. While her team of soldiers began setting up a base camp, a Space Pirate squadron had spotted them. The huntress needed to protect Platoon 83 if she were to have a chance at capturing the planet. Samus jumped out from behind the rock and fired several missiles. Explosions sent the Pirates scattering. Cries of agony could be heard amongst the smoke, and there was blood everywhere. Once the smoke cleared, all of the enemies were dead.

Or, so Samus thought. There was one Zebesian left, but it was missing an arm, lying on the ground, bleeding heavily, and apparently trying not to scream. Samus approached the injured Space Pirate and aimed her arm cannon at it. Her victim's eyes opened wide in shock, then closed. The Zebesian had accepted it's fate. As Samus charged her beam, a very old memory surfaced.

(_Twenty Years Earlier_)

Ridley surveyed his surroundings. K-2L was in a panic as his strike team laid waste to the mining colony. All was going as planned, and his mission would soon be over.

Suddenly, there was a very small voice to his left. "Excuse me, mister?"

The sight before Ridley's eyes almost made him laugh. It was a little human girl around three years old. She did not seem afraid of Ridley, to the dragon's great puzzlement.

"What do _you_ want? Can't you see I'm in the middle of something important?" He growled.

"Y-You seem nice, mister. Can we be friends?"

_Who the hell IS this? Does she not see anything around her?_

That thought barely crossed his mind when Ridley heard sniggering behind him. He turned to see many of his soldiers standing there, watching.

And this human had just humiliated him in front of them.

"Why, you little-"

"Samus, RUN!"

Ridley exhaled a breath of fire at her, but another human, this one an adult, pushed her out of the way and took the attack.

He turned again to face his minions. "What are you _doing_? Finish the mission, fools!"

About an hour later, K-2L had been almost completely destroyed. Samus was the only survivor.

(_End of Flashback_)

Samus shrugged the thought off and focused on her soon-to-be victim. Yet, another memory hit her. This was of her second mission, on SR388.

(_Five Years Earlier_)

The Queen Metroid roared, then fell to the ground, dead. Smoke billowed from Samus' arm cannon as she stepped into the next part of the cave. Upon arrival, a spherical object on the ground cracked, then shattered. It was a Metroid egg, and the baby hovered before her. Her first instinct was to shoot it, but Samus remembered her being the one survivor of K-2L's assault. This Metroid reminded Samus... of herself. Sighing, Samus let the baby follow her back to the ship.

(_End of Flashback_)

Those two memories made Samus tremble. She wanted to finish off the injured Space Pirate, but couldn't bring herself to. Then, something extremely odd happened.

"If you are going to shoot me, do it already!"

The Zebesian was talking in a human language. For a moment, Samus thought she was imagining it, but the Pirate spoke again.

"Are you deaf? Do you not understand me? Or are you trying to torture me?"

"N-no! It's just..."

Samus could not believe that she was speaking to a Space Pirate. It was hard to describe.

"What, I can talk English? Yes, it is unusual for my kind."

Coming to her senses, Samus aimed at the Pirate again.

"It's also unusual for me to let your kind survive. Beg for your life, scum!" She said coldly.

Her prey replied sarcastically. "Great, we are back on topic."

Not knowing what to think, Samus bent down and hoisted the Pirate over her shoulders.

"What are you doing?"

"I'm going to take you back to my base camp. You need medical attention."

The Zebesian struggled. "Wait! You cannot take me there! The soldiers will kill me!"

Samus stopped walking. "You're right... But, I can't just leave you here..."

She looked around and saw a distant cave. "We'll go there. I have an idea."

(_Later_)

The wind speed was increasing by the time Samus got to the cave. She set down the Space Pirate and pulled out a communicator.

"Captain, are you there?"

There was short static, then a reply. "Ferana here. Samus, where are you? It seems that a sandstorm is coming."

"I can't make it back in time. I've found a place to stay for the night, and will return in the morning."

"Roger that. Over and out."

Samus turned off the communicator and sat next to the Space Pirate, examining his wounds. They were bad, but were no longer bleeding.

"Tomorrow, I'll get a medical kit from the soldiers and try to heal you."

"T-Thank you..." He tried to respond.

"Samus. Samus Aran. Tell me... What's _your_ name?"

The Zebesian pondered her question. "I am Troop 69125. You may call me T'nar."

A rumble followed by a roar came from outside.

"What was that?" Samus asked.

T'nar replied in a quiet, yet frantic voice. "Don't make too much noise! It might hear you!"

Silence.

He let out a sigh of relief after a moment. "You see, many creatures live below the surface of this planet. What you just heard was something we have nicknamed the Death Worm."

T'nar's response shocked Samus. It seemed that the Space Pirates were the least of her concerns.

"I hope Platoon 83 is okay..."

Noticing that T'nar had fallen asleep, Samus decided to do so as well.

(_End of Chapter_)

**Author's Note: Okay! The chapters will hopefully be about this long from now on!**

**IMPORTANT UPDATE: The title of this fic will be changed in a few days. On 7/20/12, I will change the name to "An Unlikely Ally".**


	4. A Series of Unfortunate Events

Chapter 4: A Series of Unfortunate Events

**Author's Note: I want to point out something. Part of this chapter will serve as sort of a sequel to _Marx's Mad Plan_. That is all, so without further ado… Lights, camera, action!**

Samus set out for the base camp, with T'nar following her. She could not get Captain Ferana on the communications line, and was curious as to why.

"Samus? May I ask something?"

"Sure, go ahead."

T'nar hesitated, almost as if afraid to ask. "When I lay helpless and at your mercy, you did not kill me. Why?"

Samus gasped slightly at his question. "W-well… Do you remember the raid on K-2L?"

"I did not partake in it, but yes."

The very thought of that disaster brought tears to her eyes. "K-2L was my home planet. When Ridley arrived, he killed everyone, or so he thought. I survived, but at the loss of my family and friends."

Her one-armed, Zebesian ally bowed his head. "I see… I wish there was something I could do…"

Samus continued. "I left you alive because you were the last survivor of your group. You reminded me too much of myself. On top of all that, you are missing an arm… because of me."

T'nar shook his head. "I do not blame you for dismembering me. You were just doing your job."

Suddenly, he heard shouting. They were more Space Pirates, and spoke in their native Zebesian language.

"What are they saying?" Asked Samus.

"Something along the lines of, 'I found him! I found the traitor!' They keep alerting each other of someone."

It took him a while to realize that HE was the supposed turncoat.

"What? No! That's not true! Why?"

Samus grabbed his remaining arm and ran off, pulling T'nar as she went. "I don't understand… Why do they not trust me?"

The Space Pirate captain addressed his men in their language.

"Let them go. We will kill them in time. Now, we must report back to base."

(_Later_)

Samus stopped in her tracks upon arrival at the base camp. T'nar sighed and shook his head. The soldiers were dead. All of them.

"How could this have happened?"

T'nar examined the bodies. "They do not seem to have been shot. It must have been the Death Worm from last night."

"I am now alone in my mission, then…"

"That's not true, Samus. I will accompany you."

The huntress turned to face T'nar. "You… you would do that?"

He nodded. "Where else could I go? Because we were seen, I am considered a traitor. I have nothing else to do."

They went into her ship. "Thank you… I mean it. Stay here for now. I'll go get medical supplies from the camp."

After Samus left, T'nar looked at the ship's computer. It was on, so he looked at it. The screen showed a human program known as the Email System. Curiosity overcame the Zebesian, and he read the most recent messages. What he saw amazed him.

(A Few Minutes Later)

**(Author's Note: Here's the part I was talking about!)**

Samus reentered her ship to find T'nar exactly where she left him. The huntress held a bag full of odd metal parts.

"Turns out they had a kit to install mechanical limbs. Stay still and I'll do so."

As she worked, T'nar couldn't help asking about the messages he saw.

"Samus?"

"What is it?"

He responded, obviously ashamed of snooping. "While you were gone, I noticed your ship's computer was on. It seems that right before we attacked you, you were sending a message to someone by the name of Lucario. Who is that?"

If Samus was not wearing her helmet, T'nar would have seen her turn bright red. The Super Smash Brothers tournament was how she and Lucario met, and was currently on hold. Soon, the fourth tournament would begin.

T'nar continued. "As I read the message, it became clear that you two are more than simple friends."

"That's right. He is…"

The Zebesian tried to help. "Your mate?"

**(Author's Note: LMAO as I'm writing this!)**

It was a very awkward conversation.

"N-no… Not quite…"

T'nar did his equivalent of shrugging. "It is none of my concern, I assume."

"Well, it is, in a way. He tried destroying the universe to stop someone from taking over. It didn't work, however. We ended up defeating the real villain anyway."

The Zebesian almost jumped up. "HE was the cause of the antimatter?"

"Yes."

He soon calmed down. "Alright…"

Within an hour, T'nar's robotic limb was complete. He moved it around, testing it.

"Thank you, Samus. I will do all I can to assist you in your mission."

(_End of Chapter_)

**Author's Note: This story probably won't be as long as _Marx's Mad Plan_, perhaps a few more chapters at the most. See you next time! **


	5. The Mission Begins

Chapter 5: The Mission Begins

**Author's Note: Our heroes' mission will be spread out over three chapters. Lights, camera, action!**

It was nearly midday as Samus listened to T'nar point out various entrances to the Space Pirate fortress, which was underground.

"Our best option would be the northwest entrance, as it is weakly guarded, nearby, and rarely used."

The Zebesian gestured towards another part of the holographic map.

"Security is tight in these hallways, so we will have to move through ventilation shafts. They should take us to the main power generator, where I will plant an explosive. Once that is taken care of, we can proceed in eliminating the Space Pirates."

Samus nodded. "Let's get moving. We need to get there before sundown."

(_Later_)

Being a desert planet, the two were bound to find quicksand pits on it. T'nar looked closely at each before stopping at one.

"This is it. Come on."

He stepped in, to Samus' amazement, and disappeared. She decided to trust him and followed. After a few moments, Samus felt herself falling. T'nar caught her right before she hit the ground.

"Your suit makes a lot of noise, so try to be more careful. Here's a vent opening. Can you fit?"

To answer his question, Samus rolled into Morph Ball. The Zebesian lifted her up and placed her in the vent. She rolled through it, while he crawled, occasionally giving a command to turn. There was an opening ahead, and T'nar signaled that they had reached their destination. Exiting the shaft and turning back to normal, Samus scouted the area as her ally got out of the vent.

"Stand back, I shall plant the explosive on the generator."

He did so, and immediately went back into the vent.

"You had better get back in here, or else you will go along with it."

She nodded and hid in another vent. There was a beep, then an loud bang. As the two retreated into the shadows of their hiding place, a squad of Space Pirates rushed in to investigate. All of the lights went out soon after, providing an opportunity to attack. Soon, the investigators were dead.

"Nicely done, T'nar. What's next?"

He turned on the map again. "With the main generator destroyed, we should remove the auxiliary power stations. It will not take long for them to find out what happened."

(_Twenty Minutes Later_)

T'nar had planted explosives on every auxiliary power station. He figured that the plan would go better that way, instead of eliminating them one by one. If that was the case, then the Space Pirates would add extra security to each.

"Samus, get back into the vent."

She did so, and T'nar detonated the bombs. Subsequently, the base shook violently. They exited the shaft and took out the map again.

"Now that all of their power is gone, we should head to the medical wing. The last thing we need is for them to recover."

As the two walked down the corridor, Samus asked something.

"Who is in charge of this base?"

"General Agranell. He is incredibly powerful, as well as cunning. We had best be careful if we are to confront him.

"Does he have any powers of note?"

To her surprise, T'nar actually shivered.

"Agranell can tap into your mind and make you suffer horribly. That is how he punishes his men."

There was silence for a few moments before the Zebesian continued.

"He ordered our scientists to perform genetic mutation experiments on… Never mind. We've arrived at the med center. Do you have any powerful explosives? I have run out."

Samus turned into Morph Ball and snuck in before placing a Power Bomb. It went off, and cries of agony could be heard.

"Good work, now we have one more place to go before the command center, the laboratory. Agranell's secret weapon is currently under construction there."

(_End of Chapter_)

**Author's Note: T'nar mentioned genetic mutations. The guinea pig for those, you ask? You'll have to wait and see. By the way, the next chapter won't be out for a while. Sorry!**


	6. T'nar's Secret

**Author's Note: First and foremost, I'd like to point something out to anonymous viewer "Slime". Your comment would technically have given very helpful tips to writers like me, but I was planning something that would solve your problems. Samus might seem very OOC, but there's a reason for that. Read the chapter to find out. Sorry for taking so long!**

Samus and T'nar walked towards the labs silently, intent on destroying whatever the Zebesians decided to mutate. The former Space Pirate would not tell Samus what it was, and she did not ask. Upon arrival, they found the door to be closed and locked. T'nar stepped forward and tore a gap in it using his mechanical claw. One of the Zebesian scientists looked in his direction and said something. Samus made out the name "Agranell" in its sentence.

"T'nar? What's he talking about?"

Her ally was merely chuckling in his odd, alien fashion.

"I am quite surprised you haven't guessed already. Do you _really_ know me?"

"W-What?!"

The Zebesian turned around and spoke.

"He was welcoming me back, and saying that the test subjects have not had any difficulties with the mutation experiments."

Samus couldn't tell if she was more surprised or angry.

"So, you're…"

"Your thoughts are correct, Samus. I am General Agranell!"

(_Meanwhile, on the G.F.S. Olympus_)

Admiral Dane ran to one of the men operating the monitors.

"What's happening?! Why isn't Samus responding?!"

"That's the problem, sir! We can't get her on the communications line!"

(_Back in the lab_)

"I… can't… believe it…"

T'nar, no, General Agranell responded with a laugh.

"Did you ever wonder _why_ you were so trusting of me? I told you I could tamper with the minds of other life-forms. Now, I will release the test subjects and have them murder you… brutally!"

He pulled a lever, and several large glass containers fell from the ceiling. They smashed open upon contact with the floor, and released things that Samus hoped she would never see again. Things she hoped were completely extinct. But who was she kidding? They always seemed to come back.

"Metroids?!"

She was correct. However, these Metroids were different. Their outer membranes were black rather than green, and their inner nuclei were blue.

"See here, the end result of a perfect mutation experiment! About a day before you destroyed SR388, our scouts were there. They found an old Chozo record of the Metroids being created, and brought them here. We used the records to create our own, and then modified them with a mixture of Phazon and our own blood. Let's see what you make of them!"

Samus instantly switched to her Ice Beam and fired repeatedly. This, however, had absolutely no effect. The mutant Metroids dove to attack, but narrowly missed. They crashed into a box that seemed to give off warmth, which caused them to recoil and slightly shrivel up. That gave Samus an idea. She turned into Morph Ball and placed a Power Bomb. When it went off, she heard the shrieks and howls of the Metroids and Space Pirate scientists. Only Agranell was unharmed, and only he remained.

"You've had so much practice with Metroids; I'm not surprised you had it easy here. Very well, I will kill you myself."

(_End of Chapter_)

**Author's Note: Again, I am truly sorry that this took so long. However, I have not given up on this story. If I ever ****_do_**** give up on anything, I will be sure to say so. I'll get the next chapter ASAP, okay?**


	7. The Final Showdown

**Author's Note: Here's the last part of the mission! I tried to make this as descriptive as I could!**

Agranell assumed a battle stance and charged. Samus narrowly avoided him. She turned and fired Missiles, but he grabbed them with his robotic arm and lobbed them back, just barely missing Samus. With an expression of fury, Agranell jumped to the ceiling and clung to it. He pulled out a remote and pressed a button on it. There was a loud clank somewhere outside the room, and the last of the lights turned off. Samus could hear a sound that grew louder as it approached the laboratory. The door burst open, and the huntress found herself staring into the eyes of the most horrific creature she had ever seen.

"What do you think?" Agranell jeered. "_This_ is a Death Worm!"

Said creature could not have been less than thirty feet long. Its scales were a pale orange color and covered with brown spots. Simply looking at its face was enough to drive anyone into hysterics. The eyes, which were a fierce green, scanned the room. This creature more resembled a snake than a worm. It had a malformed beak, and what resembled a mane, only flaming. The Death Worm's eyes landed on Agranell, and it lunged at him with surprising speed for its size. Taking the opportunity, Samus slipped out the room and immediately ran, activating her Speed Booster adaptation. Behind her, she heard Agranell's screams and the worm's howls. A moment later, something flashed through her mind.

"No… I have to fight it…"

It was an image of her with T'nar while undergoing the mission. Agranell was obviously tampering with her thoughts so as to escape.

_Help me, Samus! I made a mistake! I should never have betrayed you! I am still T'nar!_

The thoughts were overwhelming. Regardless of what Samus did, she couldn't fight it. She turned around and ran back to the laboratory. Upon entrance, she found the Death Worm waiting for her. Agranell was nowhere to be seen. Samus jumped over the creature and shot at it. The blasts merely rebounded off its scales. Recalling her battle with the Metroid Queen on SR388, she turned into Morph Ball and rolled into the Death Worm's mouth. Samus placed her last Power Bomb in its stomach. There was a flash, then a screech, and the worm imploded. Its innards were splayed across the room, and Samus came to on the floor. Agranell lay only a few feet away from her, his legs missing.

"Ugh… Help… Samus…"

She decided to leave him there and find the command center. As she walked through the corridors, more images appeared in her head. She saw Ridley killing her parents, the Metroid hatchling sacrificing itself, and the thought that Lucario, her soul mate, was evil. Within minutes she sank to her knees, distraught.

_Why do you continue living with such horrors in your past?_

_Stop… Get out of my head, Agranell!_

However, due to his power, Samus actually did have thoughts of suicide.

_Galactic Federation soldiers have arrived. They are in this room with me. Shall I tamper with them too?_

_If they're smart, they'd kill you immediately._

_Ah, but that's the catch. I will leave you for now. Perhaps I may have the soldiers serve me… Oh? One of them seems to be on first-name terms with you. Anthony Higgs, he says his name is. Do you know him?_

_Anthony?! He's here?!_

Samus about-faced and ran as fast as she could towards the lab. She charged through the door and aimed at Agranell. However, she could not seem to shoot.

_Adorable. You still fall prey to my power. Now, answer my question. Why do you continue living?_

He was shocked to see Samus charging her beam.

_I continue living because there are people who want me to. Goodbye, Agranell._

The blast fired, and Agranell, the Space Pirate General, fell dead. Sure enough, several GF soldiers were there.

"Princess? You alright?"

The unmistakable voice of Anthony Higgs came from one.

"I… I'm fine…"

(Later)

Samus pulled the last soldier out of the quicksand pit and ran as the base self-destructed behind her.

"Anthony? How did you know where to find the base?"

He chuckled. "Well, not all of the strike team died. We would have been lost had it not been for Silent Treatment here."

Anthony gestured too his right, and Samus recognized the sniper from Ferana's group. He slowly and silently nodded.

"Well, we've captured this planet and retrieved the mineral we need. Let's go.

(_End of Chapter_)

**Author's Note: Next chapter is the last chapter! See you then!**


	8. The End?

**Author's Note: Here's the last chapter! After this comes one of my more ambitious projects!**

Samus walked up to Admiral Dane holding the mineral sample. The mission was over. She could not, however, forget about General Agranell, his lie, and the memories that he forced her to relive.

"You have done well, Samus. In only two days, you captured the planet! Naturally, you will be rewarded handsomely. For now, however, I suggest you get some sleep. You could use it."

They saluted to one another, and then parted ways. Samus returned to her ship, pondering on what to do next. Upon entrance, Adam, the central computer, spoke.

**"Lady, you have received a message."**

"Thanks… I'll check it out…"

Samus turned on the display and read the message.

_"Heard about your mission. Nice work on that! I'm currently working with a group of other Pokemon. Signups for the next Super Smash Bros. Tournament are soon! Let's hope we both get accepted!"_

_-Lucario_

She smiled to herself and remembered her final words to Agranell.

"Well… I was right about that. People _do_ want me in their lives."

Samus sent a message back.

_"Good to hear from you. We're allowed to bring a visitor with us, so if either of us doesn't make the cut, we can still spend time together. Hope to see you soon."_

_-Samus_

**"I have picked up a distress signal from a nearby planet. Shall I direct the ship there?"**

"I'll go tomorrow. First, I need to pick up my reward from Admiral Dane."

**"Very well. Good night, Lady"**

(Meanwhile… on the desert planet…)

The squad of Zebesian soldiers entered the hidden laboratory. In their own language, they alerted their leader.

"Commander Velnaw, sir! We've found General Agranell!"

A yellow-scaled Space Pirate stepped inside and observed the body.

"Well, he always did boast of his 'invincibility', the fool. The Galactic Federation can have this planet. We have already obtained what we need. Bring the experimental Metroid DNA back to the ship. There is much for us to do…"

(_End_)

**Author's Note: Okay! That ends this story! Next time you hear from me, it'll be my new Pokemon fanfiction. See you guys then!**


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